

# data_path=

brca12=brca12
brca44=brca44
lunca50=cancer50


genome_name=grch37.fa
genome_brca12_name=brca12.b37.fasta
genome_brca44_name=brca44.b37.fasta
genome_lunca50_name=lunca50.b37.fasta

if test -z "$ref_genome"; then


if [ "$interval" = "$brca12" ]; then
	# export ref_genome=${data_path}/ref/b37/brca12/$genome_brca12_name # meet a problem with this as ref_genome in gatk coverage statistics.
	export ref_genome=${data_path}/ref/b37/b37.fa
	#echo ref_genome: $ref_genome
elif [ "$interval" = "$brca44" ]; then
	export ref_genome=${data_path}/ref/b37/brca44/$genome_brca44_name
	#echo ref_genome: $ref_genome
elif [ "$interval" = "$lunca50" ]; then
	export ref_genome=${data_path}/ref/b37/lunca50/$genome_lunca50_name
	#echo ref_genome: $ref_genome
elif test "$asemmbly" = "b38"; then
	export ref_genome=${data_path}/ref/b38/b38.fa
	#echo ref genome: $ref_genome
	export genome_assembly=b38
elif test "$assembly" = "b38"; then
	export ref_genome=${data_path}/ref/b38/b38.fa
	#echo ref genome: $ref_genome
	export genome_assembly=b38
elif test "$assembly" = "38"; then
	export ref_genome=${data_path}/ref/b38/b38.fa
	#echo ref genome: $ref_genome
	export genome_assembly=b38
elif test "$asemmbly" = "38"; then
	export ref_genome=${data_path}/ref/b38/b38.fa
	#echo ref genome: $ref_genome
	export genome_assembly=b38
else
	export ref_genome=${data_path}/ref/b37/$genome_name
	#echo ref_genome: $ref_genome
fi

fi

echo ref_genome: $ref_genome
